Contacts of the helix formed by residues 404 - 410 (chain C) in PDB entry 3GZN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 404 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C TRP* 3.6 48.7 - - - -
170C ARG* 3.0 8.5 + - - -
172C ILE* 4.2 1.6 - - - -
402C CYS 3.5 2.6 + - - -
403C ARG* 1.3 76.8 - - - +
405C LEU* 1.3 63.5 + - - +
406C ALA* 3.5 9.3 + - - +
407C GLU* 3.0 35.9 + - - +
408C GLU 3.4 11.3 + - - -
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C SER* 4.0 22.7 - - - +
144C LEU* 4.0 20.6 - - + +
147C ALA* 3.6 35.6 + - + +
151C TRP* 6.1 0.4 - - - +
159C ILE* 4.0 9.6 - - + -
168C TYR* 5.0 4.0 - - - +
170C ARG* 4.0 21.2 - - + +
172C ILE* 4.4 9.4 - - + +
404C SER* 1.3 71.4 - - - +
406C ALA* 1.3 66.0 + - - +
408C GLU* 3.1 24.3 + - - +
409C TYR* 3.0 45.6 + - + +
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Residues in contact with ALA 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU* 5.1 6.4 - - + +
147C ALA* 5.6 0.4 - - - +
148C ASP* 5.0 13.7 - - + +
404C SER* 3.3 8.6 + - - +
405C LEU* 1.3 76.7 - - - +
407C GLU* 1.3 53.4 + - - +
409C TYR* 4.2 4.7 - - - +
410C GLY* 2.8 32.4 + - - -
413C THR* 4.0 0.7 + - - -
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Residues in contact with GLU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C TRP* 5.2 3.9 - - - -
403C ARG* 3.1 43.9 + - - +
404C SER* 3.0 40.8 + - - +
405C LEU 3.2 0.2 - - - -
406C ALA* 1.3 74.9 - - + +
408C GLU* 1.3 64.7 + - - +
409C TYR 3.3 0.7 + - - -
410C GLY 3.3 1.2 + - - -
413C THR* 2.7 39.4 + - + +
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Residues in contact with GLU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TYR* 4.3 5.2 + - - -
170C ARG* 2.6 42.1 + - - +
403C ARG* 3.6 2.8 - - - +
404C SER 3.4 1.6 + - - -
405C LEU* 3.1 18.6 + - - +
407C GLU* 1.3 78.2 - - - +
409C TYR* 1.3 68.9 + - + +
414C ILE* 3.9 23.8 - - + +
433C TYR* 2.6 40.6 + - - +
437C ARG* 4.3 5.0 + - - -
475C TYR* 4.8 0.2 - - - -
526C THR* 4.5 0.5 + - - -
541C LEU* 3.3 39.4 + - + +
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Residues in contact with TYR 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLU* 3.6 32.2 + - + +
144C LEU* 3.9 28.7 - - + -
168C TYR* 5.4 4.9 + - - -
405C LEU* 3.0 44.5 + - + +
406C ALA* 4.2 2.9 - - - +
408C GLU* 1.3 90.9 - - + +
410C GLY* 1.3 66.9 + - - +
411C LEU* 3.5 2.3 + - - +
433C TYR* 4.3 2.2 - + - -
437C ARG* 3.2 52.2 + - - +
440C ASP* 4.4 7.4 + - - -
475C TYR* 2.4 28.0 + - - -
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Residues in contact with GLY 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C ALA 2.8 18.1 + - - -
407C GLU 3.3 1.8 + - - -
409C TYR* 1.3 79.0 - - - +
411C LEU* 1.3 65.7 + - - -
412C ASP 3.2 2.9 - - - -
413C THR* 3.4 11.4 - - - -
414C ILE* 3.1 20.3 + - - +
475C TYR* 3.8 4.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il